adding falcon (#5057)
* py-networkx: adding older version py-networkx * py-pypeflow: new package * falcon: adding new package pacbio-daligner: adding new package pacbio-damasker: adding new package pacbio-dazz-db: adding new package pacbio-dextractor: adding new package * py-networkx: modifying version order to be in line with convention * falcon: tweaking py-networkx dependency to satisfy setuptools py-pypeflow: adding missing dependency * pacbio-dextractor: changing hdf5 dependency * pacbio-daligner: adding gmake build dep pacbio-damasker: adding gmake build dep pacbio-dazz-db: adding gmake build dep pacbio-dextractor: adding gmake build dep
This commit is contained in:
parent
9e7917f7d3
commit
64a32ea1f9
51
var/spack/repos/builtin/packages/falcon/package.py
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51
var/spack/repos/builtin/packages/falcon/package.py
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class Falcon(PythonPackage):
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"""Falcon: a set of tools for fast aligning long reads for consensus
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and assembly.
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The Falcon tool kit is a set of simple code collection which I use
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for studying efficient assembly algorithm for haploid and diploid genomes.
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It has some back-end code implemented in C for speed and some simple
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front-end written in Python for convenience."""
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homepage = "https://github.com/PacificBiosciences/FALCON"
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url = "https://github.com/PacificBiosciences/FALCON.git"
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version('2017-05-30',
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git='https://github.com/PacificBiosciences/FALCON.git',
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commit='86cec6157291679095ea6080b0cde6561eccc041')
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depends_on('py-setuptools', type='run')
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depends_on('py-pypeflow', type='run')
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depends_on('py-networkx@1.7:1.10', type=['build', 'run'])
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depends_on('pacbio-dazz-db', type='run')
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depends_on('pacbio-daligner', type='run')
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depends_on('pacbio-dextractor', type='run')
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depends_on('pacbio-damasker', type='run')
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48
var/spack/repos/builtin/packages/pacbio-daligner/package.py
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48
var/spack/repos/builtin/packages/pacbio-daligner/package.py
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class PacbioDaligner(MakefilePackage):
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"""Daligner: The Dazzler "Overlap" Module. This is a special fork
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required for some pacbio utilities."""
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homepage = "https://github.com/PacificBiosciences/DALIGNER"
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url = "https://github.com/PacificBiosciences/DALIGNER"
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version('2017-08-05',
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git='https://github.com/PacificBiosciences/DALIGNER.git',
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commit='0fe5240d2cc6b55bf9e04465b700b76110749c9d')
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depends_on('gmake', type='build')
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depends_on('pacbio-dazz-db')
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def edit(self, spec, prefix):
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mkdir(prefix.bin)
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makefile = FileFilter('Makefile')
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makefile.filter('DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin)
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gmf = FileFilter('GNUmakefile')
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gmf.filter('rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
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'cp ${ALL} ' + prefix.bin)
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47
var/spack/repos/builtin/packages/pacbio-damasker/package.py
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var/spack/repos/builtin/packages/pacbio-damasker/package.py
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class PacbioDamasker(MakefilePackage):
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"""Damasker: The Dazzler Repeat Masking Suite. This is a special fork
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required for some pacbio utilities."""
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homepage = "https://github.com/PacificBiosciences/DAMASKER"
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url = "https://github.com/PacificBiosciences/DAMASKER"
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version('2017-02-11',
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git='https://github.com/PacificBiosciences/DAMASKER.git',
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commit='144244b77d52cb785cb1b3b8ae3ab6f3f0c63264')
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depends_on('gmake', type='build')
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def edit(self, spec, prefix):
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mkdirp(prefix.bin)
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makefile = FileFilter('Makefile')
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makefile.filter('DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin)
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gmf = FileFilter('GNUmakefile')
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gmf.filter('rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
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'cp ${ALL} ' + prefix.bin)
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55
var/spack/repos/builtin/packages/pacbio-dazz-db/package.py
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55
var/spack/repos/builtin/packages/pacbio-dazz-db/package.py
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class PacbioDazzDb(MakefilePackage):
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"""The Dazzler Database Library. This version is a special fork
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required for some pacbio utilities."""
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homepage = "https://github.com/PacificBiosciences/DAZZ_DB"
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url = "https://github.com/PacificBiosciences/DAZZ_DB"
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version('2017-04-10',
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git='https://github.com/PacificBiosciences/DAZZ_DB.git',
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commit='f29d27d51f460563481cd227d17f4bdc5e288365')
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depends_on('gmake', type='build')
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def edit(self, spec, prefix):
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mkdirp(prefix.bin)
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mkdirp(prefix.lib)
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mkdirp(prefix.include)
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makefile = FileFilter('Makefile')
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makefile.filter('DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin)
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gmf = FileFilter('GNUmakefile')
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gmf.filter('rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
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'cp ${ALL} ' + prefix.bin)
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gmf.filter('rsync\s*-av\s*libdazzdb.*\s*\$\{PREFIX\}/lib',
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'cp libdazzdb.* ' + prefix.lib)
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gmf.filter(('rsync\s*-av\s*\$\(wildcard\s*\$\{THISDIR\}/\*.h'
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'\)\s*\$\{PREFIX\}/include'),
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'cp *.h ' + prefix.include)
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class PacbioDextractor(MakefilePackage):
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"""The Dextractor and Compression Command Library. This is a special
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fork required by some pacbio utilities."""
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homepage = "https://github.com/PacificBiosciences/DEXTRACTOR"
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url = "https://github.com/PacificBiosciences/DEXTRACTOR"
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version('2016-08-09',
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git='https://github.com/PacificBiosciences/DEXTRACTOR.git',
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commit='89726800346d0bed15d98dcc577f4c7733aab4b1')
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depends_on('hdf5')
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depends_on('gmake', type='build')
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def edit(self, spec, prefix):
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mkdirp(prefix.bin)
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makefile = FileFilter('Makefile')
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makefile.filter('PATH_HDF5\s*=\s*/sw/apps/hdf5/current',
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'PATH_HDF5 = ' + spec['hdf5'].prefix)
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makefile.filter('PATH_HDF5\*s=\s*/usr/local/hdf5', '')
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makefile.filter('DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin)
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gmf = FileFilter('GNUmakefile')
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gmf.filter('rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
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'cp ${ALL} ' + prefix.bin)
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url = "https://pypi.io/packages/source/n/networkx/networkx-1.11.tar.gz"
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version('1.11', '6ef584a879e9163013e9a762e1cf7cd1')
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version('1.10', 'eb7a065e37250a4cc009919dacfe7a9d')
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depends_on('py-decorator', type=('build', 'run'))
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depends_on('py-setuptools', type='build')
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40
var/spack/repos/builtin/packages/py-pypeflow/package.py
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40
var/spack/repos/builtin/packages/py-pypeflow/package.py
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class PyPypeflow(PythonPackage):
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"""pypeFLOW is light weight and reusable make / flow data process
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library written in Python."""
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homepage = "https://github.com/PacificBiosciences/pypeFLOW"
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url = "https://github.com/PacificBiosciences/pypeFLOW"
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version('2017-05-04',
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git='https://github.com/PacificBiosciences/pypeFLOW.git',
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commit='f23a1b290876bbdf130611000934ae4247158073')
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depends_on('py-setuptools', type='build')
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depends_on('py-networkx@1.7:1.11', type=['build', 'run'])
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